DNA Subway: Making Genome Analysis Egalitarian

Abstract

DNA Subway bundles research-grade bioinformatics tools, high-performance computing, and databases into easy-to-use workflows. Students have been "riding" different lines since 2010, to predict and annotate genes in up to 150kb of raw DNA sequence (Red Line), identify homologs in sequenced genomes (Yellow Line), identify species using DNA barcodes and construct phylogenetic trees (Blue Line), and examine RNA sequence (RNA-Seq) datasets for transcript abundance and differential expression (Green Line). With support for plant and animal genomes, DNA Subway engages students in their own learning, bringing to life key concepts in molecular biology, genetics, and evolution. Integrated DNA barcoding and RNA extraction wet-lab experiments support a variety of inquiry-based projects using student-generated data. Products of student research can be exported, published, and used in follow-up experiments. To date, DNA Subway has over 8,000 registered users who have produced 51,000 projects. Based on the popular Tuxedo Protocol, the Green Line was introduced in January 2014 as an easy-to-use workflow to analyze RNA-Seq datasets. The workflow uses iPlant's APIs (http://agaveapi.co/) to access high-performance compute resources of NSF's Extreme Scientific and Engineering Discovery Environment (XSEDE), providing the first easy "on ramp" to biological supercomputing.